Hi Matt!
Running stores that I know of in SJ area ~ there is the Road Runners chain on Hamilton and Bascom in Campbell and about 1/2 mile away also in Campbell is Running Revolution. They're on Campbell Ave and a small independent store, but they know a lot and have a decent selection. I don't know how often, but I they've done group runs on Saturday mornings before.
Next to Running Revolution is an area called the Par Course. It's a park and they have paved/nonpaved trail that will take you from Campbell into Los Gatos, but not sure how far out it goes, but at least 4/5 miles out. In Los Altos off 280 (freeway), about 5 miles north of SJ there are trails called Rancho San Antonio. There are a lot of paths, all train and a really good hill for hill training. I haven't gone yet, but want to, is a place called Communication Hill in SJ. I believe it's off 85 and if you google it you can easily fnd info on it. It's a residential area, but there is one hill and a lot of people go out there for training runs. If you're feeling adventurous, you could always drive up to San Francisco early in the morning on the weekends for a run. I do that sometimes. If you go close to the water, there's an area called Marina Green and there is parking there and you pretty much follow the water and can go all the to the bridge and back. If you go the opposite way you can run a good distance on the Embarcadero out to AT&T Park.
Oh! Nice part about being out here is if you need to fly anywhere, we have 3 airports you can play w/ for cheap prices and times. (Definitely helps when planning WDW runs

) SFO will have the most delays of the 3 b/c of the fog, but you can fly out/in out of there the latest.
For food, you pretty much can find everything and anything in ways of cuisine. Downtown SJ has a lot of restuarants and bars/clubs. Another popular area is Santana Row. It's an outdoor shopping area, but there are good restuarants and bars and it's always packed at night.
Sportswise, the Sharks Arena (hockey) is downtown, Raiders/A's/Warriors are at the Coliseum about 45-50 minutes away, Giants are 45-1 hour depending on traffic, but their minor league team in in SJ and tickets are really cheap and games are fun, 49ers new stadium opens in Santa Clara this year and the Earthquakes (soccer) are opening a new stadium soon near the SJ airport.
That's all I can think of for now, but if I think of anything or you have any questions ask away!